Overview | Package | Class | Use | Tree | Deprecated | Index | Help
PREV LETTER NEXT LETTER | FRAMES NO FRAMES

A B C D E F G H I K L M N O P Q R S T U V W X Y Z

## A

A2Xml - Class in org.metaqtl.main
A2Xml() - Constructor for class org.metaqtl.main.A2Xml
absolute() - Method in interface org.thalia.bio.util.ILGroupPosition
absolute() - Method in class org.thalia.bio.util.LGroupPosition
adapt(Chromosome[]) - Static method in class org.metaqtl.adapter.MetaQtlAnalysisAdapter
adapt(EMResult) - Static method in class org.metaqtl.adapter.QtlAdapter
  From a result of a EM clustering returns the mixture components as an array of Qtl.
adapt(MetaQtlData) - Static method in class org.metaqtl.adapter.QtlPartitionAdapter
  Adapt the given `MetaQtlData` into a `QtlPartition` and returns it.
adapt(MetaQtlAnalysis, String, String, int) - Static method in class org.metaqtl.adapter.QtlPartitionAdapter
  Adapt the `MetaQtlAnalysis` `analysis` for a given value of the number of clusters `k` and a given trait name `code`.
adapt(MetaQtlResult, Qtl[], int) - Static method in class org.metaqtl.adapter.QtlPartitionAdapter
addAllele(IBioAllele) - Method in class org.thalia.bio.entity.AlleleContainer
addAllele(IBioAllele) - Method in interface org.thalia.bio.IBioLocus
addAllMap(IBioGenome[]) - Method in class org.metaqtl.MapCluster
addBooleanOption(char, String) - Method in class org.metaqtl.main.CmdLineParser
  Convenience method for adding a boolean option.
addBooleanOption(String) - Method in class org.metaqtl.main.CmdLineParser
  Convenience method for adding a boolean option.
addChild(TreeNode) - Method in class org.metaqtl.TreeNode
  Add a child to the node.
addChromosome(IBioLGroup, IBioCross, int, int, boolean, boolean) - Method in class org.metaqtl.ChromCluster
  Add a chromosome to the cluster
addChromosome(IBioLGroup, IBioCross, int, int, boolean, boolean) - Method in class org.metaqtl.MapCluster
  Add a chromosome to the map cluster framework.
addDoubleOption(char, String) - Method in class org.metaqtl.main.CmdLineParser
  Convenience method for adding a double option.
addDoubleOption(String) - Method in class org.metaqtl.main.CmdLineParser
  Convenience method for adding a double option.
addEdge(Chromosome, Chromosome, CMarkerSequence) - Method in class org.metaqtl.ChromCluster.ClusterGraph
addGroup(IBioLGroup) - Method in class org.thalia.bio.entity.GroupContainer
addGroup(IBioLGroup) - Method in interface org.thalia.bio.IBioGenome
addIndividual(IBioIndividual) - Method in class org.thalia.bio.entity.IndividualContainer
addIndividual(IBioIndividual) - Method in interface org.thalia.bio.IBioPopulation
addIntegerOption(char, String) - Method in class org.metaqtl.main.CmdLineParser
  Convenience method for adding an integer option.
addIntegerOption(String) - Method in class org.metaqtl.main.CmdLineParser
  Convenience method for adding an integer option.
additive - Variable in class org.metaqtl.Qtl.QTLStats
  The additive effect of the QTL.
addLocus(IBioLocus) - Method in class org.thalia.bio.entity.LocusContainer
addLocus(IBioLocus) - Method in interface org.thalia.bio.IBioLGroup
addLongOption(char, String) - Method in class org.metaqtl.main.CmdLineParser
  Convenience method for adding a long integer option.
addLongOption(String) - Method in class org.metaqtl.main.CmdLineParser
  Convenience method for adding a long integer option.
addMap(IBioGenome, boolean) - Method in class org.metaqtl.MapCluster
  Add a map to the cluster.
addOption(CmdLineParser.Option) - Method in class org.metaqtl.main.CmdLineParser
  Add the specified Option to the list of accepted options
addQtl(Graphics2D, QtlUnit) - Method in class org.metaqtl.graph.QtlLayerBuffer
  Try to add a qtl unit to the configuration.
addStringOption(char, String) - Method in class org.metaqtl.main.CmdLineParser
  Convenience method for adding a string option.
addStringOption(String) - Method in class org.metaqtl.main.CmdLineParser
  Convenience method for adding a string option.
addTerm(String, String) - Method in class org.metaqtl.MetaDico
adjTable - Variable in class org.metaqtl.ChromCluster.ClusterGraph
AIC - Static variable in class org.metaqtl.EMCriteria
aic - Variable in class org.metaqtl.EMCriteria
AIC3 - Static variable in class org.metaqtl.EMCriteria
aic3 - Variable in class org.metaqtl.EMCriteria
AIC3_NAME - Static variable in class org.metaqtl.EMCriteria
AIC_NAME - Static variable in class org.metaqtl.EMCriteria
AICc - Static variable in class org.metaqtl.EMCriteria
aicc - Variable in class org.metaqtl.EMCriteria
AICc_NAME - Static variable in class org.metaqtl.EMCriteria
ALIGN_FIRST_COMMON - Static variable in class org.metaqtl.graph.ChromLayer
ALIGN_FIRST_MARKER - Static variable in class org.metaqtl.graph.ChromLayer
alignChromLayers(ChromLayer, ChromLayer, int) - Static method in class org.metaqtl.graph.ChromLayer
ALLELE - Static variable in interface org.thalia.bio.IBioEntityTypes
  The integer code for Allele entity
AlleleContainer - Class in org.thalia.bio.entity
  Class Description Here
AlleleContainer() - Constructor for class org.thalia.bio.entity.AlleleContainer
AlleleContainer(String, IBioEntity) - Constructor for class org.thalia.bio.entity.AlleleContainer
alleles() - Method in class org.thalia.bio.entity.AlleleContainer
alleles() - Method in interface org.thalia.bio.IBioLocus
AnchoredElement - Class in org.metaqtl.graph
AnchoredElement() - Constructor for class org.metaqtl.graph.AnchoredElement
areMarkersAroundQTL(int, int, int) - Method in class org.metaqtl.Chromosome
  Returns true if the QTL position is inside the marker interval which markers indices are `mrkIdxL` and `mrkIdxR`.
attach(Object) - Method in class org.metaqtl.graph.ChromLayer
attach(Object) - Method in class org.metaqtl.graph.Layer
  Attach the given `object` to the layer.
attach(Object) - Method in class org.metaqtl.graph.QtlLayer
attach(Object) - Method in class org.metaqtl.graph.QtlPartitionLayer
attach(Object) - Method in class org.metaqtl.graph.QtlTreeLayer
attachQtl(Qtl[]) - Method in class org.metaqtl.Chromosome
attachQTL(IBioLocus[]) - Method in class org.metaqtl.Chromosome
  Add
AWE - Static variable in class org.metaqtl.EMCriteria
awe - Variable in class org.metaqtl.EMCriteria
AWE_NAME - Static variable in class org.metaqtl.EMCriteria

Overview | Package | Class | Use | Tree | Deprecated | Index | Help
PREV LETTER NEXT LETTER | FRAMES NO FRAMES

A B C D E F G H I K L M N O P Q R S T U V W X Y Z